The genes in the mouse H-2 major histocompatibility complex (MHC) determine a diversity of functions associated with immune recognition and reaction. Several genes in this region e.g. H-2K, D, L and R encode antigens involved in allograft rejection and T-lymphocyte responses. The purpose of this work is to determine the primary structure of these molecules in order to better understand their function and mechanism of action. The determination of the 346 amino acid residue, H-2K(D) membrane-bound molecule has been completed. For comparative purposes, major portions of the primary structure of four other H-2 molecules have been determined. These studies indicate that most of the amino acid sequence differences among these molecules are localized to discrete regions. In addition, H-2 molecules have been found to vary in length and in the number of carbohydrate prosthetic groups that they possess. Sequential immunoprecipitation studies have revealed the presence of a previously unidentified D-region molecule in the d and q haplotypes (H-2R). Elucidation of the complete primary structure of murine B2m has revealed a genetic dimorphism: an Ala-Asp interchange occurring at position 85.